3ARB

Ternary crystal structure of the NKT TCR-CD1d-alpha-galactosylceramide analogue-OCH


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.216 

wwPDB Validation   3D Report Full Report


This is version 2.1 of the entry. See complete history


Literature

A molecular basis for the exquisite CD1d-restricted antigen specificity and functional responses of natural killer T cells

Wun, K.S.Cameron, G.Patel, O.Pang, S.S.Pellicci, D.G.Sullivan, L.C.Keshipeddy, S.Young, M.H.Uldrich, A.P.Thakur, M.S.Richardson, S.K.Howell, A.R.Illarionov, P.A.Brooks, A.G.Besra, G.S.McCluskey, J.Gapin, L.Porcelli, S.A.Godfrey, D.I.Rossjohn, J.

(2011) Immunity 34: 327-339

  • DOI: https://doi.org/10.1016/j.immuni.2011.02.001
  • Primary Citation of Related Structures:  
    3ARB, 3ARD, 3ARE, 3ARF, 3ARG

  • PubMed Abstract: 

    Natural killer T (NKT) cells respond to a variety of CD1d-restricted antigens (Ags), although the basis for Ag discrimination by the NKT cell receptor (TCR) is unclear. Here we have described NKT TCR fine specificity against several closely related Ags, termed altered glycolipid ligands (AGLs), which differentially stimulate NKT cells. The structures of five ternary complexes all revealed similar docking. Acyl chain modifications did not affect the interaction, but reduced NKT cell proliferation, indicating an affect on Ag processing or presentation. Conversely, truncation of the phytosphingosine chain caused an induced fit mode of TCR binding that affected TCR affinity. Modifications in the glycosyl head group had a direct impact on the TCR interaction and associated cellular response, with ligand potency reflecting the t(1/2) life of the interaction. Accordingly, we have provided a molecular basis for understanding how modifications in AGLs can result in striking alterations in the cellular response of NKT cells.


  • Organizational Affiliation

    The Protein Crystallography Unit, ARC Centre of Excellence in Structural and Functional Microbial Genomics, Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, Victoria 3800, Australia.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Antigen-presenting glycoprotein CD1d1302Mus musculusMutation(s): 0 
Gene Names: Cd1d1Cd1.1
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Go to UniProtKB:  P11609
IMPC:  MGI:107674
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UniProt GroupP11609
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-2-microglobulin99Mus musculusMutation(s): 0 
Gene Names: B2m
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Find proteins for P01887 (Mus musculus)
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Go to UniProtKB:  P01887
IMPC:  MGI:88127
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UniProt GroupP01887
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
NKT Valpha14-Jalpha18,NKT Valpha14-Jalpha18207Mus musculusHomo sapiens
This entity is chimeric
Mutation(s): 0 
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Find proteins for P01848 (Homo sapiens)
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Go to UniProtKB:  P01848
PHAROS:  P01848
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UniProt GroupP01848
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
NKT Vbeta8.2,NKT Vbeta8.2244Mus musculusHomo sapiens
This entity is chimeric
Mutation(s): 0 
UniProt
Find proteins for P01850 (Homo sapiens)
Explore P01850 
Go to UniProtKB:  P01850
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UniProt GroupP01850
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 5
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
E, F, G
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
FEE PDBBind:  3ARB Kd: 234 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.216 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.037α = 90
b = 87.309β = 90
c = 235.654γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
PHASERphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-03-30
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2014-01-29
    Changes: Database references
  • Version 1.3: 2020-01-22
    Changes: Advisory, Database references, Derived calculations, Source and taxonomy, Structure summary
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2023-11-01
    Changes: Data collection, Database references, Refinement description, Structure summary